More details are needed to answer this question, e.g. what type of pathogens are you looking at (bacteria, virus, ...). We have carried out similar work looking at virus-host interactions in human pathogens, with the aim to identify novel drug targets and therapeutic strategies. This was done using a combination of high throughput experiments and computational modeling. What ressources do you have available to do this? are you looking at a purely computational approach, or ability to carry out experiments?

I am actually co-coordinator of an EU-funded research project on this very topic. You can find some more information at http://www.syspatho.eu

This is exactly the approach of my previous research group http://www2.warwick.ac.uk/fac/sci/lifesci/research/presta/ , work is ongoing, but you can see the publications for an idea of current progress. I think the answer is that it is feasible, but will probably take a long time and considerable resources.

Hi,

We assess this question on the virus-human interaction model by combining both experimental approach (Yeast two-hybrid screens between pathogen ORF and human cDNA libraries) and computational approach. The idea is to better characterise and identify critical nodes for the viral infection within the whole cellular network in order to provide systems biology rational for drug design.

To have an idea of what can be done, see virhostnet, a curated protein-protein interaction ressource for virus-host interactome, mainly focused on human viruses: http://pbildb1.univ-lyon1.fr/virhostnet/index.php

For the pathogen-plant system see Mukhtar MS, Carvunis AR et al. an excelent paper in science from the Vidal Lab. (http://www.ncbi.nlm.nih.gov/pubmed/21798943).

Hope it will help,

I am interested in the same approach in humans, in particular I am looking for data related to interactions among human and bacterial proteins. I already know the work from Dryer, Sobral et al ( http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012089 ; http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.0040032 ), but these works are usually focused on dangerous bacteria only, such as anthracis, and not on 'normal' bacteria, that can be a concomitant cause of human pathologies. I am particularly intrigued by 'hi-thru' molecular docking techniques but I am not an expert of this field.

PATRIC is a nice resource http://www.patricbrc.org/portal/portal/patric/Home

I have software (SLiMFinder and QSLiMFinder) for finding common motifs between, which can be used to look for pathogenic proteins mimicking host proteins. (See http://www.ncbi.nlm.nih.gov/pubmed/21146412 for a good review of these.) The software is available free here (http://www.southampton.ac.uk/~re1u06/software/packages/slimsuite/) and I can help you get it working if it looks useful. Input would be a set of pathogenic and/or host proteins that all interact with a common partner (normally a host protein).

We did some previous work in this, looking at effectors from bacterial and oomycete pathogens, and their interactions with Arabidopsis proteins:

http://www.sciencemag.org/content/333/6042/596.full

Thank you all for your useful contributions. Though the question wasn't asked by me, I nevertheless enjoy all the contributions from the senior scientists and professors here. I like your good spirits. I'm also working on a similar project in humans for a PhD at the University of Manchester. I find your contributions useful. I may need to contact some of you in the future.

Dear all eminent scientists and experts across the globe,

I am overwhelmed by the response to study the plant microbe-interaction. Thank you so much for your inspirational and valuable comments. Now I can think that it is possible to study the plant-microbe interaction ..in many ways...

Thank you all...

I need to go though the above mentioned research papers then only I can comment and..do my work.

Fungi problem needs an excess of humidity for example.

I'm involved in the NIH NIAIDs Systems Biology centers, which are working on these kinds of problems for human pathogens. Many of these approaches will be similar for plant-pathogen interactions.

Computational methods to provide clear answers to questions such as the one you pose above (Can computational biologists working across the globe recommend ways to enhance the productivity of crops against these notorious crop pathogens?) are dependent on the data available for the system, and are generally not at a sufficient level of maturity to be able to answer such questions in detail. Rather, these approaches are very valuable to guide experimentalists to novel hypotheses by identification of important nodes (genes, proteins metabolites), pathways, and interactions. The hypotheses can then be followed up on (validated) to gain novel insight into the system.

The main website for these centers is:

http://www.niaid.nih.gov/labsandresources/resources/dmid/sb/pages/default.aspx

Dear Sir Jason Mcdermott , Thank you very much for response. As I have such interest to study-plant microbe interaction, I want to know up to much we are now in this field? How much success we have gained so far? I would alos like to know whether is there any scope for this kind work any other parts of the country besides my home country India. If any eminent scientist working on this field, I would like to know from there group. what is the possible approach?

Plant-microbe interactions are studied by a number of groups. In Germany, for example, the Max Planck Society has a whole institute devoted to this type of questions in Cologne (Max Planck Institute for Plant Breeding Research); similarly, the Leibniz-Institute for plant genetics (IPK) in Gatersleben works on related problems, and has a large Computational Biology department. You will find additional information and contacts on their websites

Plant-microbe interactions studies offer an interesting molecular view on disease progression and resistance especially when systems biology tools or effector and LRR domain (R proteins) mining approaches are used. However if you are looking towards engineering disease resistant crops, I will suggest the new and effective quantitative genomics approach called GENOMIC SELECTION. It builds on estimation of breeding values and selection based on SNPs allowing for incorporation of Mendelian sampling during Genomic Estimated Breeding Value prediction. With this approach you can engineer plants which can effectively combine innate immunity (against a wide range of diseases) with increased production and quality products.

Take a look at this review http://www.ncbi.nlm.nih.gov/pubmed/22420640

Dear Uche Okeke,

Sir do you have any idea bout the tools are available to mine effctor and the resistance genes from the published pathogen and plant genomes. If you have any idea regrading the interaction study about the plant-microbe using system biology approach would be a valuable resource for understanding the molecular biology behind the disease resistance in plants.

Effector and resistance gene (R gene) mining is a domain mining problem (pattern matching). You try to find the amino acid repeats in your effector virulence protein domain and or use the known LRR repeat region of the R-gene to mine for interacting domains across the genome. Note that the interacting pattern you are searching for will be based on a prior biological knowledge.

see this paper where LRR genes are mined throughout the genome.

http://www.pnas.org/content/108/suppl.1/4631.full